U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    NRPD1B nuclear RNA polymerase D1B [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 818591, updated on 18-Sep-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    NRPD1B
    Official Full Name
    nuclear RNA polymerase D1B
    Primary source
    TAIR:AT2G40030
    Locus tag
    AT2G40030
    See related
    Araport:AT2G40030
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING 5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B; T28M21.19; T28M21_19
    Summary
    Encodes the unique largest subunit of nuclear DNA-dependent RNA polymerase V; homologous to budding yeast RPB1 and the E. coli RNA polymerase beta prime subunit. Required for normal RNA-directed DNA methylation at non-CG methylation sites and transgene silencing.
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See NRPD1B in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    18
    Sequence:
    Chromosome: 2; NC_003071.7 (16714460..16723718)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Ribosomal protein L10 family protein Neighboring gene Nucleolar histone methyltransferase-related protein Neighboring gene Cysteine/Histidine-rich C1 domain family protein Neighboring gene Clathrin light chain protein Neighboring gene flocculation FLO11-like protein

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Kanno T, et al. Nat Genet, 2005 Jul. PMID 15924141
    2. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Mosher RA, et al. Proc Natl Acad Sci U S A, 2008 Feb 26. PMID 18287047, Free PMC Article
    3. The role of DNA (de)methylation in immune responsiveness of Arabidopsis. López Sánchez A, et al. Plant J, 2016 Nov. PMID 27341062, Free PMC Article
    4. NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis. Eamens A, et al. Plant J, 2008 Aug. PMID 18433438
    5. PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Lahmy S, et al. Proc Natl Acad Sci U S A, 2009 Jan 20. PMID 19141635, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DRD1-Pol V-dependent de novo methylation may play a role in restraining the inappropriate silencing of active protein-coding genes in plants. [NRPE1]
      Title: DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene.
    2. Genome-wide chromatin association of NRPE1 is dependent on all members of a putative chromatin-remodeling complex termed DDR, which includes the proteins DRD1, DMS3 and RDM1.
      Title: DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.
    3. Mutants defective for the NRPD1a and NRPD1b alternative largest subunits of polymerase IV were tested for their ability to undergo RNA silencing and mantenance of transcription and post-transcriptional silencing.
      Title: NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help
    NM_001336818.1
    NM_129561.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within defense response to fungus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulatory ncRNA-mediated post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA processing IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase IV complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of RNA polymerase V complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of RNA polymerase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    nuclear RNA polymerase D1B
    NP_181532.2
    • nuclear RNA polymerase D1B (NRPD1B); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF3223 (InterPro:IPR021602), RNA polymerase, N-terminal (InterPro:IPR006592), RNA polymerase, alpha subunit (InterPro:IPR000722), RNA polymerase Rpb1, domain 3 (InterPro:IPR007066), RNA polymerase Rpb1, domain 1 (InterPro:IPR007080), RNA polymerase Rpb1, domain 5 (InterPro:IPR007081); BEST Arabidopsis thaliana protein match is: nuclear RNA polymerase D1A (TAIR:AT1G63020.2); Has 52919 Blast hits to 31940 proteins in 6835 species: Archae - 366; Bacteria - 10380; Metazoa - 13235; Fungi - 6920; Plants - 7147; Viruses - 757; Other Eukaryotes - 14114 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003071.7 Reference assembly

      Range
      16714460..16723718
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_129561.4 → NP_181532.2  nuclear RNA polymerase D1B [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_181532.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O04206, O04207, Q1L5X4, Q5D869
      UniProtKB/TrEMBL
      A0A178VUS8
      Conserved Domains (5) summary
      cd02737
      Location:825 → 1231
      RNAP_IV_NRPD1_C; Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
      smart00663
      Location:204 → 500
      RPOLA_N; RNA polymerase I subunit A N-terminus
      cd10506
      Location:24 → 798
      RNAP_IV_RPD1_N; Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain
      pfam10427
      Location:1526 → 1655
      Ago_hook; Argonaute hook
      pfam11523
      Location:1752 → 1825
      DUF3223; Protein of unknown function (DUF3223)

    2. NM_001336818.1 → NP_001323985.1  nuclear RNA polymerase D1B [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VWE9, A0A1P8AYR1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5D869.1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.